Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMCs]

ABSTRACT: High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMCs]

PROVIDER: PRJNA658080 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12476601_1.fastq.gz	Fastqsanger.gz
	SRR12476601_2.fastq.gz	Fastqsanger.gz
	SRR12476602_1.fastq.gz	Fastqsanger.gz
	SRR12476602_2.fastq.gz	Fastqsanger.gz
	SRR12476603_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

High throughput joint profiling of chromatin accessibility and protein levels in single cells

Project description:High throughput joint profiling of chromatin accessibility and protein levels in single cells

| PRJNA658075 | ENA

High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMC_Stim_Multiome]

Project description:High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMC_Stim_Multiome]

| PRJNA699556 | ENA

High throughput joint profiling of chromatin accessibility and protein levels in single cells [Tcell_Intra]

Project description:High throughput joint profiling of chromatin accessibility and protein levels in single cells [Tcell_Intra]

| PRJNA699565 | ENA

High throughput joint profiling of chromatin accessibility and protein levels in single cells [marrow]

Project description:High throughput joint profiling of chromatin accessibility and protein levels in single cells [marrow]

| PRJNA658082 | ENA

High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMC stimulation]

Project description:High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMC stimulation]

| PRJNA658078 | ENA

High throughput joint profiling of chromatin accessibility and protein levels in single cells [Tcell KO]

Project description:High throughput joint profiling of chromatin accessibility and protein levels in single cells [Tcell KO]

| PRJNA658083 | ENA

High throughput joint profiling of chromatin accessibility and protein levels in single cells [Species mix]

Project description:High throughput joint profiling of chromatin accessibility and protein levels in single cells [Species mix]

| PRJNA658084 | ENA

High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMCs]

Project description:Recent technological advances have enabled massively parallel single-cell Assay for Transposase Accessible Chromatin by sequencing (scATAC-seq) to simultaneously profile the epigenomic landscape in thousands of individual cells. scATAC-seq methods sample genomic DNA accessible to transposases, but have not previously been combined with measurement of protein levels. Here, we present ATAC with Select Antigen Profiling by sequencing, ASAP-seq, a tool to simultaneously profile accessible chromatin and protein levels in thousands of single cells, pairing sparse scATAC data with robust detection of hundreds of cell surface and intracellular protein markers, and optionally, enriched mtDNA coverage for lineage tracing (mtscATAC-seq) with minimal impact on ATAC-seq data quality. ASAP-seq makes use of a novel bridging approach to utilize existing commercially available antibody:oligo conjugates developed for CITE-seq and related technologies. We demonstrate the utility of ASAP-seq in the context of hematopoietic differentiation, cell surface marker dynamics following peripheral blood mononuclear cell stimulation, and as a combinatorial decoder of multiplexed perturbations in primary T cells.

2020-09-08 | GSE156474 | GEO

Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling

Project description:MultiPerturb-seq is a high-throughput CRISPR screening platform with joint single nucleus chromatin accessibility, transcriptome, and guide RNA capture. It uses combinatorial indexing combined with droplet microfluidics to scale throughput and integrate all three modalities. We apply MultiPerturb-seq to identify key genes whose loss can trigger differentiation in a rare pediatric cancer, atypical teratoid/rhabdoid tumor (AT/RT), which is driven by loss of the SWI/SNF chromatin remodeling subunit SMARCB1.

2024-09-22 | GSE277747 | GEO

Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-cell Levels II

Project description:We report the development of a novel method called EpiVIA (https://github.com/VahediLab/epiVIA) for the joint profiling of the chromatin accessibility and lentiviral integration site analysis at the population and single-cell levels. We validate our technique in clonal cells with previously defined integration sites and further demonstrate the ability to measure lentiviral integration sites and chromatin accessibility of host and viral genomes at the single-cell resolution in CAR-T cells. We anticipate that EpiVIA will enable the single-cell deconstruction of gene regulation during CAR-T therapy, leading to the discovery of cellular factors associated with durable treatment.

2020-01-15 | GSE143646 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data